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. 2011:2011:878973.
doi: 10.1155/2011/878973. Epub 2011 Aug 8.

Cross-Genome Comparisons of Newly Identified Domains in Mycoplasma gallisepticum and Domain Architectures with Other Mycoplasma species

Chandra Sekhar Reddy Chilamakuri  1 , Adwait Joshi, Sane Sudha Rani, Bernard Offmann, R Sowdhamini
Affiliations

Cross-Genome Comparisons of Newly Identified Domains in Mycoplasma gallisepticum and Domain Architectures with Other Mycoplasma species

Chandra Sekhar Reddy Chilamakuri et al. Comp Funct Genomics. 2011.

Abstract

Accurate functional annotation of protein sequences is hampered by important factors such as the failure of sequence search methods to identify relationships and the inherent diversity in function of proteins related at low sequence similarities. Earlier, we had employed intermediate sequence search approach to establish new domain relationships in the unassigned regions of gene products at the whole genome level by taking Mycoplasma gallisepticum as a specific example and established new domain relationships. In this paper, we report a detailed comparison of the conservation status of the domain and domain architectures of the gene products that bear our newly predicted domains amongst 14 other Mycoplasma genomes and reported the probable implications for the organisms. Some of the domain associations, observed in Mycoplasma that afflict humans and other non-human primates, are involved in regulation of solute transport and DNA binding suggesting specific modes of host-pathogen interactions.

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Figures

Figure 1
Figure 1
Multiple sequence alignment between peptidase_M23 family representative sequences and unassigned protein sequence (NP_853190.1) from M. gallisepticum genome. Peptidase_M23 sequences obtained from Pfam database. Characteristic HxH motif is conserved and has few insertion regions in the unassigned sequence.
Figure 2
Figure 2
Peptidase domain presence in different Mycoplasma genomes. Domain represented by square box and species by circle. Lines connecting domain and species indicate the presence of domain in that species. Edge numbers indicate number of domains copies in genome.
Figure 3
Figure 3
Multiple sequence alignment between Lactamase_b family representative sequences and unassigned protein sequence (NP_852865.1) from M. gallisepticum genome. Lactamase_b sequences obtained from Pfam database.
Figure 4
Figure 4
Multiple sequence alignment between RMMBL family representative sequences and unassigned protein sequence (NP_852865.1) from M. gallisepticum genome. RMMBL sequences obtained from Pfam database.
Figure 5
Figure 5
Presence of RMMBL and Lactamase_B domains and domain architecture in different Mycoplasma genomes. Domains are in square box and species in the circles. Edges represent presence of that domain in that species.
Figure 6
Figure 6
Comparison of SBP_bac_5 domain across different Mycoplasma genomes. SBP_bac_5 domain present in all the Mycoplasma genomes but in Mycoplasma mobile, Mycoplasma pneumoniae, and Mycoplasma synoviae. All the genomes have single copy of SBP_bac_5 domain except Mycoplasma mycoides and Mycoplasma capricolum where two copies were found in the genome.
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